I think the majority of medical schools will not see it as a separate A-Level. Majority will, however, accept it as a 4th AS-Level, and if they don't they may just give you a higher offer with the new reforms.
I think quite a few say that if you do take it, they will not count it as a separate subject, and for your grade, will take the average grade of the two, so if you got an A* in Maths, but a B in FMaths, you would be counted as having achieved an A. Others will completely disregard it. I think there will be a few who do take it into account, though, but it really isn't necessary.
I do somewhat agree with the stance that it isn't exactly an extra subject, since it is literally just more maths. That said, I still wasn't willing to continue on with FMaths, doing 4 subjects myself due to the workload, uncertainty and increased difficulty from AS to A-Level, which actually would have been evident from what I'd heard, unlike what I'd found from GCSE to AS.